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Implementation of fetch_pdb() #4943
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I'm not sure where to put this code in the codebase, so I create a new folder for it right now. I'm open to it being moved somewhere Some stuff which I like to still add (besides tests and docs):
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I think others will have to confirm, but likely we'll want to have Additional it's not finalised yet but if the mmcif reader in #2367 gets finalised then the default download shouldn't be |
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## develop #4943 +/- ##
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- Coverage 93.86% 93.86% -0.01%
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Files 179 179
Lines 22249 22267 +18
Branches 3161 3165 +4
===========================================
+ Hits 20885 20901 +16
- Misses 902 903 +1
- Partials 462 463 +1 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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I'm ok with that. I can make the code raise an exception if |
Assuming that |
You've added it to one of the optional dependency categories which is all that should be required. For the actual files where it is used you'll need to have something setup like the usage of biopython: mdanalysis/package/MDAnalysis/analysis/align.py Lines 200 to 207 in dcaa087
I'm not an expert on the pipelines so someone else would have to pitch in more on that. |
Thanks for the comment! |
I happen to have another question! Is it normal for some of the tests to not be consistent across each commit? From what I understand, each github CLI has to get and build each MDAnalysis from source, and this instance can potentially timeout from what I observe across each commit. The macOS (of the latest commit) failed at 97% of test because it reached the max wall time of two hours. Even then the latest Azure tests failed because of other tests in the source code which I didn't write (namely due to other tests)
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In principle, tests should pass everywhere. The Azure tests time out in the test
which looks like something that you added. I haven't looked at your code but it might simply be the case that some stuff needs to be written differently for windows. |
@jauy123 do you have time to pick up this PR again? Would be great to have the feature in 2.10! |
I have time again. I was busy starting the end of spring break with comps, classes, and you know what. |
…since text files are just binary files with special encoding
…est_gsd_reader_raises
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From my side of things, this looks good to me!
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Ah nearly forgot! Can you update the changelog & authors please!
Fixes #4907
Changes made in this Pull Request:
This is a still work in progress, but here's a implementation of @BradyAJohnston 's code wrapped into classes. I still need to write tests and docs for the entire thing.
DownloaderBase
and 'PDBDownloader' in order to implement downloading structure file from online sources such as the PDB databank.requests
as a dependencymda.fetch_pdb()
is implemented as a wrapper to commonly used option in 'PDBDownloader'PR Checklist
package/CHANGELOG
file updated?Developers Certificate of Origin
I certify that I can submit this code contribution as described in the Developer Certificate of Origin, under the MDAnalysis LICENSE.
📚 Documentation preview 📚: https://mdanalysis--4943.org.readthedocs.build/en/4943/